search

icub-tech-iit / ergocub-gazebo-simulations

Repository containing the models and the simulations for ergoCub
BSD 3-Clause "New" or "Revised" License
4 stars 0 forks source link

Problems in loading stickbot with urdf parser py #49

Closed CarlottaSartore closed 10 months ago

CarlottaSartore commented 10 months ago

I am having issues in loading the stickbot urdf in urdf parser py, due to the declaration of XML encoding

https://github.com/icub-tech-iit/ergocub-gazebo-simulations/blob/1179630a88541479df51ebb108a21865ea251302/models/stickBot/model.urdf#L1

see attached log:

Errort

___ ERROR collecting tests/parametric/test_NumPy_computations_parametric.py ____ ../../../micromamba/envs/adamdev/lib/python3.11/site-packages/_pytest/runner.py:341: in from_call result: Optional[TResult] = func() ../../../micromamba/envs/adamdev/lib/python3.11/site-packages/_pytest/runner.py:372: in call = CallInfo.from_call(lambda: list(collector.collect()), "collect") ../../../micromamba/envs/adamdev/lib/python3.11/site-packages/_pytest/python.py:531: in collect self._inject_setup_module_fixture() ../../../micromamba/envs/adamdev/lib/python3.11/site-packages/_pytest/python.py:545: in _inject_setup_module_fixture self.obj, ("setUpModule", "setup_module") ../../../micromamba/envs/adamdev/lib/python3.11/site-packages/_pytest/python.py:310: in obj self._obj = obj = self._getobj() ../../../micromamba/envs/adamdev/lib/python3.11/site-packages/_pytest/python.py:528: in _getobj return self._importtestmodule() ../../../micromamba/envs/adamdev/lib/python3.11/site-packages/_pytest/python.py:617: in _importtestmodule mod = import_path(self.path, mode=importmode, root=self.config.rootpath) ../../../micromamba/envs/adamdev/lib/python3.11/site-packages/_pytest/pathlib.py:567: in import_path importlib.import_module(module_name) ../../../micromamba/envs/adamdev/lib/python3.11/importlib/__init__.py:126: in import_module return _bootstrap._gcd_import(name[level:], package, level) :1204: in _gcd_import ??? :1176: in _find_and_load ??? :1147: in _find_and_load_unlocked ??? :690: in _load_unlocked ??? ../../../micromamba/envs/adamdev/lib/python3.11/site-packages/_pytest/assertion/rewrite.py:186: in exec_module exec(co, module.__dict__) tests/parametric/test_NumPy_computations_parametric.py:63: in comp = KinDynComputations(model_path, joints_name_list, root_link) ../../../micromamba/envs/adamdev/lib/python3.11/site-packages/adam/numpy/computations.py:32: in __init__ factory = URDFModelFactory(path=urdfstring, math=math) ../../../micromamba/envs/adamdev/lib/python3.11/site-packages/adam/model/std_factories/std_model.py:24: in __init__ self.urdf_desc = urdf_parser_py.urdf.URDF.from_xml_file(path) ../../../micromamba/envs/adamdev/lib/python3.11/site-packages/urdf_parser_py/xml_reflection/core.py:617: in from_xml_file return cls.from_xml_string(xml_string) ../../../micromamba/envs/adamdev/lib/python3.11/site-packages/urdf_parser_py/xml_reflection/core.py:610: in from_xml_string node = etree.fromstring(xml_string) src/lxml/etree.pyx:3257: in lxml.etree.fromstring ??? src/lxml/parser.pxi:1911: in lxml.etree._parseMemoryDocument ???

This is an output of a CI (see https://github.com/CarlottaSartore/ADAM/actions/runs/6783258175), In my setup it does not happen, I attach here the conda list

Working Env Conda List

``` # packages in environment at /home/carlotta/miniforge3/envs/ADAM_env: # # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_kmp_llvm conda-forge absl-py 1.4.0 pyhd8ed1ab_0 conda-forge ace 7.1.1 h59595ed_0 conda-forge adam-robotics 0.0.8.dev19 pypi_0 pypi alsa-lib 1.2.10 hd590300_0 conda-forge ampl-mp 3.1.0 h2cc385e_1006 conda-forge aom 3.5.0 h27087fc_0 conda-forge assimp 5.2.5 hf40c2ba_0 conda-forge asttokens 2.2.1 pyhd8ed1ab_0 conda-forge attr 2.5.1 h166bdaf_1 conda-forge backcall 0.2.0 pyh9f0ad1d_0 conda-forge backports 1.0 pyhd8ed1ab_3 conda-forge backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge binutils 2.39 hdd6e379_1 conda-forge binutils_impl_linux-64 2.39 he00db2b_1 conda-forge binutils_linux-64 2.39 h5fc0e48_12 conda-forge boost-cpp 1.78.0 h2c5509c_4 conda-forge brotli 1.0.9 h166bdaf_8 conda-forge brotli-bin 1.0.9 h166bdaf_8 conda-forge brotlipy 0.7.0 py310h5764c6d_1005 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.18.1 h7f98852_0 conda-forge c-compiler 1.5.2 h0b41bf4_0 conda-forge ca-certificates 2023.7.22 hbcca054_0 conda-forge cairo 1.18.0 h3faef2a_0 conda-forge casadi 3.6.3 py310h528c296_0 conda-forge certifi 2023.7.22 pyhd8ed1ab_0 conda-forge cffi 1.15.1 py310h255011f_3 conda-forge charset-normalizer 3.1.0 pyhd8ed1ab_0 conda-forge cloudpickle 2.2.1 pypi_0 pypi cmake 3.26.3 h077f3f9_0 conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge comodo 0.0.1 pypi_0 pypi compilers 1.5.2 ha770c72_0 conda-forge contourpy 1.0.7 py310hdf3cbec_0 conda-forge cppad 20230000.0 hcb278e6_0 conda-forge cryptography 40.0.2 py310h34c0648_0 conda-forge curl 8.4.0 hca28451_0 conda-forge cxx-compiler 1.5.2 hf52228f_0 conda-forge cycler 0.11.0 pyhd8ed1ab_0 conda-forge dataclasses 0.8 pyhc8e2a94_3 conda-forge dav1d 1.2.1 hd590300_0 conda-forge dbus 1.13.6 h5008d03_3 conda-forge decorator 5.1.1 pyhd8ed1ab_0 conda-forge eigen 3.4.0 h4bd325d_0 conda-forge entrypoints 0.4 pypi_0 pypi etils 1.5.1 pyhd8ed1ab_0 conda-forge exceptiongroup 1.1.3 pyhd8ed1ab_0 conda-forge executing 1.2.0 pyhd8ed1ab_0 conda-forge expat 2.5.0 hcb278e6_1 conda-forge ffmpeg 6.0.0 gpl_hdbbbd96_103 conda-forge filelock 3.13.1 pyhd8ed1ab_0 conda-forge fmt 9.1.0 h924138e_0 conda-forge font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 3.000 h77eed37_0 conda-forge font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge font-ttf-ubuntu 0.83 hab24e00_0 conda-forge fontconfig 2.14.2 h14ed4e7_0 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge fonttools 4.39.3 py310h1fa729e_0 conda-forge fortran-compiler 1.5.2 hdb1a99f_0 conda-forge freeglut 3.2.2 hac7e632_2 conda-forge freetype 2.12.1 hca18f0e_1 conda-forge freetype-py 2.3.0 pyhd8ed1ab_0 conda-forge fribidi 1.0.10 h36c2ea0_0 conda-forge fsspec 2023.10.0 pyhca7485f_0 conda-forge future 0.18.3 pyhd8ed1ab_0 conda-forge gcc 11.3.0 h02d0930_12 conda-forge gcc_impl_linux-64 11.3.0 hab1b70f_19 conda-forge gcc_linux-64 11.3.0 he6f903b_12 conda-forge gettext 0.21.1 h27087fc_0 conda-forge gfortran 11.3.0 ha859ce3_12 conda-forge gfortran_impl_linux-64 11.3.0 he34c6f7_19 conda-forge gfortran_linux-64 11.3.0 h3c55166_12 conda-forge git 2.42.0 pl5321h86e50cf_0 conda-forge gitdb 4.0.10 pypi_0 pypi gitpython 3.1.37 pypi_0 pypi glfw 3.3.8 h166bdaf_0 conda-forge glib 2.78.1 hfc55251_0 conda-forge glib-tools 2.78.1 hfc55251_0 conda-forge gmp 6.2.1 h58526e2_0 conda-forge gmpy2 2.1.2 py310h3ec546c_1 conda-forge gnutls 3.7.8 hf3e180e_0 conda-forge graphite2 1.3.13 h58526e2_1001 conda-forge gst-plugins-base 1.22.6 h8e1006c_2 conda-forge gstreamer 1.22.6 h98fc4e7_2 conda-forge gxx 11.3.0 h02d0930_12 conda-forge gxx_impl_linux-64 11.3.0 hab1b70f_19 conda-forge gxx_linux-64 11.3.0 hc203a17_12 conda-forge harfbuzz 8.2.1 h3d44ed6_0 conda-forge hdf5 1.14.2 nompi_h4f84152_100 conda-forge icu 73.2 h59595ed_0 conda-forge icub-models 2.4.1 py310hc6cd4ac_0 conda-forge idna 3.4 pyhd8ed1ab_0 conda-forge idyntree 9.1.0 py310hcc9ab6b_1 conda-forge imageio 2.27.0 pyh24c5eb1_0 conda-forge importlib-metadata 6.8.0 pyha770c72_0 conda-forge importlib_metadata 6.8.0 hd8ed1ab_0 conda-forge importlib_resources 6.1.0 pyhd8ed1ab_0 conda-forge iniconfig 2.0.0 pyhd8ed1ab_0 conda-forge ipopt 3.14.12 hf9e1ecf_0 conda-forge ipython 8.12.0 pyh41d4057_0 conda-forge irrlicht 1.8.5 h2a6caf8_4 conda-forge jasper 4.1.0 he6dfbbe_0 conda-forge jax 0.4.19 pyhd8ed1ab_0 conda-forge jaxlib 0.4.14 cpu_py310h67d73b5_1 conda-forge jedi 0.18.2 pyhd8ed1ab_0 conda-forge jinja2 3.1.2 pyhd8ed1ab_1 conda-forge kernel-headers_linux-64 2.6.32 he073ed8_15 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.4 py310hbf28c38_1 conda-forge krb5 1.21.2 h659d440_0 conda-forge lame 3.100 h166bdaf_1003 conda-forge lcms2 2.15 hb7c19ff_3 conda-forge ld_impl_linux-64 2.39 hcc3a1bd_1 conda-forge lerc 4.0.0 h27087fc_0 conda-forge libabseil 20230125.3 cxx17_h59595ed_0 conda-forge libaec 1.0.6 hcb278e6_1 conda-forge libass 0.17.1 h8fe9dca_1 conda-forge libblas 3.9.0 16_linux64_openblas conda-forge libbrotlicommon 1.0.9 h166bdaf_8 conda-forge libbrotlidec 1.0.9 h166bdaf_8 conda-forge libbrotlienc 1.0.9 h166bdaf_8 conda-forge libcap 2.67 he9d0100_0 conda-forge libcblas 3.9.0 16_linux64_openblas conda-forge libccd-double 2.1 h27087fc_3 conda-forge libclang 15.0.7 default_h7634d5b_3 conda-forge libclang13 15.0.7 default_h9986a30_3 conda-forge libcups 2.3.3 h4637d8d_4 conda-forge libcurl 8.4.0 hca28451_0 conda-forge libdeflate 1.19 hd590300_0 conda-forge libdrm 2.4.114 h166bdaf_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge libevent 2.1.12 hf998b51_1 conda-forge libexpat 2.5.0 hcb278e6_1 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libflac 1.4.2 h27087fc_0 conda-forge libgcc-devel_linux-64 11.3.0 h210ce93_19 conda-forge libgcc-ng 12.2.0 h65d4601_19 conda-forge libgcrypt 1.10.1 h166bdaf_0 conda-forge libgfortran-ng 13.2.0 h69a702a_0 conda-forge libgfortran5 13.2.0 ha4646dd_0 conda-forge libglib 2.78.1 hebfc3b9_0 conda-forge libglu 9.0.0 he1b5a44_1001 conda-forge libgomp 12.2.0 h65d4601_19 conda-forge libgpg-error 1.46 h620e276_0 conda-forge libgrpc 1.54.2 hb20ce57_2 conda-forge libhwloc 2.9.3 default_h554bfaf_1009 conda-forge libi2c 4.3 hcb278e6_2 conda-forge libiconv 1.17 h166bdaf_0 conda-forge libidn2 2.3.4 h166bdaf_0 conda-forge libjpeg-turbo 3.0.0 hd590300_1 conda-forge liblapack 3.9.0 16_linux64_openblas conda-forge liblapacke 3.9.0 16_linux64_openblas conda-forge liblie-group-controllers 0.2.0 hcb278e6_0 conda-forge libllvm15 15.0.7 h5cf9203_3 conda-forge libllvm16 16.0.6 h5cf9203_1 conda-forge libmatio 1.5.23 h31675a7_4 conda-forge libmatio-cpp 0.2.2 h002c22a_0 conda-forge libmujoco 2.3.7 hd8909ca_0 conda-forge libnghttp2 1.52.0 h61bc06f_0 conda-forge libnsl 2.0.0 h7f98852_0 conda-forge libogg 1.3.4 h7f98852_1 conda-forge libopenblas 0.3.21 pthreads_h78a6416_3 conda-forge libopencv 4.8.1 py39h72824ba_5 conda-forge libopenvino 2023.1.0 h59595ed_1 conda-forge libopenvino-auto-batch-plugin 2023.1.0 h59595ed_1 conda-forge libopenvino-auto-plugin 2023.1.0 h59595ed_1 conda-forge libopenvino-hetero-plugin 2023.1.0 h59595ed_1 conda-forge libopenvino-intel-cpu-plugin 2023.1.0 h59595ed_1 conda-forge libopenvino-intel-gpu-plugin 2023.1.0 h59595ed_1 conda-forge libopenvino-ir-frontend 2023.1.0 h59595ed_1 conda-forge libopenvino-onnx-frontend 2023.1.0 h59595ed_1 conda-forge libopenvino-paddle-frontend 2023.1.0 h59595ed_1 conda-forge libopenvino-pytorch-frontend 2023.1.0 h59595ed_1 conda-forge libopenvino-tensorflow-frontend 2023.1.0 h59595ed_1 conda-forge libopenvino-tensorflow-lite-frontend 2023.1.0 h59595ed_1 conda-forge libopus 1.3.1 h7f98852_1 conda-forge libosqp 0.6.3 h59595ed_0 conda-forge libpciaccess 0.17 h166bdaf_0 conda-forge libpng 1.6.39 h753d276_0 conda-forge libpq 16.0 hfc447b1_1 conda-forge libprotobuf 3.21.12 hfc55251_2 conda-forge libqdldl 0.1.5 h27087fc_1 conda-forge librealsense 2.54.1 h8386552_1_cpu conda-forge librobometry 1.2.1 hc5a7426_1 conda-forge libsanitizer 11.3.0 h239ccf8_19 conda-forge libsndfile 1.2.0 hb75c966_0 conda-forge libsqlite 3.44.0 h2797004_0 conda-forge libssh2 1.11.0 h0841786_0 conda-forge libstdcxx-devel_linux-64 11.3.0 h210ce93_19 conda-forge libstdcxx-ng 12.2.0 h46fd767_19 conda-forge libsystemd0 253 h8c4010b_1 conda-forge libtasn1 4.19.0 h166bdaf_0 conda-forge libtiff 4.6.0 ha9c0a0a_2 conda-forge libudev1 253 h0b41bf4_1 conda-forge libunicycle-footstep-planner 0.6.0 h59595ed_1 conda-forge libunistring 0.9.10 h7f98852_0 conda-forge libusb 1.0.26 h0b4f0b6_100 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libuv 1.46.0 hd590300_0 conda-forge libva 2.18.0 h0b41bf4_0 conda-forge libvorbis 1.3.7 h9c3ff4c_0 conda-forge libvpx 1.13.0 hcb278e6_0 conda-forge libwebp-base 1.3.2 hd590300_0 conda-forge libxcb 1.15 h0b41bf4_0 conda-forge libxkbcommon 1.6.0 h5d7e998_0 conda-forge libxml2 2.11.5 h232c23b_1 conda-forge libxslt 1.1.37 h0054252_1 conda-forge libzlib 1.2.13 h166bdaf_4 conda-forge llvm-openmp 17.0.4 h4dfa4b3_0 conda-forge lodepng 20220109 h924138e_0 conda-forge lxml 4.9.3 py310h9b7343a_0 conda-forge lz4-c 1.9.4 hcb278e6_0 conda-forge make 4.3 hd18ef5c_1 conda-forge manif 0.0.4 hcb278e6_13 conda-forge manifpy 0.0.4 py310haded995_13 conda-forge markupsafe 2.1.3 py310h2372a71_1 conda-forge matplotlib 3.7.1 py310hff52083_0 conda-forge matplotlib-base 3.7.1 py310he60537e_0 conda-forge matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge metis 5.1.0 h58526e2_1006 conda-forge mkl 2022.2.1 h84fe81f_16997 conda-forge ml_dtypes 0.3.1 py310hcc13569_2 conda-forge mpc 1.3.1 hfe3b2da_0 conda-forge mpfr 4.2.1 h9458935_0 conda-forge mpg123 1.31.3 hcb278e6_0 conda-forge mpmath 1.3.0 pyhd8ed1ab_0 conda-forge mujoco-python 2.3.7 py310h99e3f1e_0 conda-forge mujoco-python-viewer 0.1.2 pypi_0 pypi mumps-include 5.2.1 ha770c72_11 conda-forge mumps-seq 5.2.1 h2104b81_11 conda-forge munkres 1.1.4 pyh9f0ad1d_0 conda-forge mysql-common 8.0.33 hf1915f5_6 conda-forge mysql-libs 8.0.33 hca2cd23_6 conda-forge ncurses 6.3 h27087fc_1 conda-forge nettle 3.8.1 hc379101_1 conda-forge networkx 3.1 pyhd8ed1ab_0 conda-forge ninja 1.11.1 h924138e_0 conda-forge nlohmann_json 3.11.2 h27087fc_0 conda-forge nspr 4.35 h27087fc_0 conda-forge nss 3.94 h1d7d5a4_0 conda-forge numpy 1.22.4 py310h4ef5377_0 conda-forge ocl-icd 2.3.1 h7f98852_0 conda-forge ocl-icd-system 1.0.0 1 conda-forge openh264 2.3.1 hcb278e6_2 conda-forge openjpeg 2.5.0 h488ebb8_3 conda-forge openssl 3.1.4 hd590300_0 conda-forge opt-einsum 3.3.0 hd8ed1ab_2 conda-forge opt_einsum 3.3.0 pyhc1e730c_2 conda-forge osqp-eigen 0.8.0 hdd734ac_1 conda-forge p11-kit 0.24.1 hc5aa10d_0 conda-forge packaging 23.1 pyhd8ed1ab_0 conda-forge pandas 2.0.0 pypi_0 pypi parso 0.8.3 pyhd8ed1ab_0 conda-forge pcre2 10.40 hc3806b6_0 conda-forge perl 5.32.1 4_hd590300_perl5 conda-forge pexpect 4.8.0 pyh1a96a4e_2 conda-forge pickleshare 0.7.5 py_1003 conda-forge pillow 10.1.0 py310h01dd4db_0 conda-forge pip 23.1 pyhd8ed1ab_0 conda-forge pixman 0.42.2 h59595ed_0 conda-forge pkg-config 0.29.2 h36c2ea0_1008 conda-forge platformdirs 3.2.0 pyhd8ed1ab_0 conda-forge pluggy 1.3.0 pyhd8ed1ab_0 conda-forge ply 3.11 py_1 conda-forge pooch 1.7.0 pyha770c72_3 conda-forge portaudio 19.6.0 h7c63dc7_9 conda-forge prettytable 3.7.0 pypi_0 pypi prompt-toolkit 3.0.38 pyha770c72_0 conda-forge prompt_toolkit 3.0.38 hd8ed1ab_0 conda-forge proxsuite 0.3.7 py310hd41b1e2_0 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge pugixml 1.14 h59595ed_0 conda-forge pulseaudio-client 16.1 h5195f5e_3 conda-forge pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge pybind11-abi 4 hd8ed1ab_3 conda-forge pycollada 0.7.2 pyhd8ed1ab_0 conda-forge pycparser 2.21 pyhd8ed1ab_0 conda-forge pygad 3.1.0 pypi_0 pypi pyglet 1.5.16 py310hff52083_1 conda-forge pyglfw 2.5.9 py310hff52083_0 conda-forge pygments 2.15.1 pyhd8ed1ab_0 conda-forge pyopengl 3.1.6 pyhd8ed1ab_1 conda-forge pyopenssl 23.1.1 pyhd8ed1ab_0 conda-forge pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge pyqt 5.15.7 py310hab646b1_3 conda-forge pyqt5-sip 12.11.0 py310heca2aa9_3 conda-forge pyrender 0.1.45 pyh8a188c0_3 conda-forge pysocks 1.7.1 pyha2e5f31_6 conda-forge pytest 7.4.3 pyhd8ed1ab_0 conda-forge python 3.10.10 he550d4f_0_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python_abi 3.10 3_cp310 conda-forge pytorch 2.0.0 cpu_mkl_py310h402c8e3_101 conda-forge pytz 2023.3 pypi_0 pypi pyyaml 6.0 pypi_0 pypi qhull 2020.2 h4bd325d_2 conda-forge qt-main 5.15.8 h82b777d_17 conda-forge re2 2023.03.02 h8c504da_0 conda-forge readline 8.2 h8228510_1 conda-forge requests 2.28.2 pyhd8ed1ab_1 conda-forge rhash 1.4.3 h166bdaf_0 conda-forge robot-testing-framework 2.0.1 hcb278e6_1 conda-forge scipy 1.10.1 py310h8deb116_0 conda-forge scotch 6.0.9 hb2e6521_2 conda-forge sdl 1.2.68 h293081c_0 conda-forge sdl2 2.28.4 h77f46ba_0 conda-forge setuptools 67.6.1 pyhd8ed1ab_0 conda-forge simde 0.7.6 h00ab1b0_0 conda-forge sip 6.7.8 py310heca2aa9_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge sleef 3.5.1 h9b69904_2 conda-forge smmap 5.0.1 pypi_0 pypi snappy 1.1.10 h9fff704_0 conda-forge soxr 0.1.3 h0b41bf4_3 conda-forge spdlog 1.11.0 h9b3ece8_1 conda-forge stack_data 0.6.2 pyhd8ed1ab_0 conda-forge svt-av1 1.6.0 h59595ed_0 conda-forge sympy 1.12 pypyh9d50eac_103 conda-forge sysroot_linux-64 2.12 he073ed8_15 conda-forge tbb 2021.10.0 h00ab1b0_2 conda-forge tinyxml 2.6.2 h4bd325d_2 conda-forge tinyxml2 9.0.0 h9c3ff4c_2 conda-forge tk 8.6.13 noxft_h4845f30_101 conda-forge tl-optional 1.1.0 hf52228f_1 conda-forge toml 0.10.2 pyhd8ed1ab_0 conda-forge tomli 2.0.1 pyhd8ed1ab_0 conda-forge tomlplusplus 3.3.0 hcb278e6_0 conda-forge tornado 6.3 py310h1fa729e_0 conda-forge traitlets 5.9.0 pyhd8ed1ab_0 conda-forge trimesh 3.21.5 pyhd8ed1ab_0 conda-forge typing-extensions 4.5.0 hd8ed1ab_0 conda-forge typing_extensions 4.5.0 pyha770c72_0 conda-forge tzdata 2023.3 pypi_0 pypi unicodedata2 15.0.0 py310h5764c6d_0 conda-forge unixodbc 2.3.10 h583eb01_0 conda-forge urdf-parser-py 0.0.4 pypi_0 pypi urdfmodifiers 0.0.2 pypi_0 pypi urdfpy 0.0.22 pyha21a80b_3 conda-forge urllib3 1.26.15 pyhd8ed1ab_0 conda-forge visit_struct 1.0.0.1 hcb278e6_2 conda-forge wcwidth 0.2.6 pyhd8ed1ab_0 conda-forge wheel 0.40.0 pyhd8ed1ab_0 conda-forge x264 1!164.3095 h166bdaf_2 conda-forge x265 3.5 h924138e_3 conda-forge xcb-util 0.4.0 hd590300_1 conda-forge xcb-util-image 0.4.0 h8ee46fc_1 conda-forge xcb-util-keysyms 0.4.0 h8ee46fc_1 conda-forge xcb-util-renderutil 0.3.9 hd590300_1 conda-forge xcb-util-wm 0.4.1 h8ee46fc_1 conda-forge xkeyboard-config 2.38 h0b41bf4_0 conda-forge xorg-fixesproto 5.0 h7f98852_1002 conda-forge xorg-inputproto 2.3.2 h7f98852_1002 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.1.1 hd590300_0 conda-forge xorg-libsm 1.2.4 h7391055_0 conda-forge xorg-libx11 1.8.6 h8ee46fc_0 conda-forge xorg-libxau 1.0.11 hd590300_0 conda-forge xorg-libxcursor 1.2.0 h0b41bf4_1 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge xorg-libxi 1.7.10 h7f98852_0 conda-forge xorg-libxinerama 1.1.5 h27087fc_0 conda-forge xorg-libxrandr 1.5.2 h7f98852_1 conda-forge xorg-libxrender 0.9.11 hd590300_0 conda-forge xorg-randrproto 1.5.0 h7f98852_1001 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge xorg-xf86vidmodeproto 2.3.1 h7f98852_1002 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xz 5.2.6 h166bdaf_0 conda-forge yarp 3.8.1 ha770c72_7 conda-forge yarp-cxx 3.8.1 h57bc1a5_7 conda-forge yarp-python 3.8.1 py310h6c2f4e2_7 conda-forge ycm-cmake-modules 0.15.1 hcb278e6_1 conda-forge zipp 3.17.0 pyhd8ed1ab_0 conda-forge zlib 1.2.13 h166bdaf_4 conda-forge zstd 1.5.5 hfc55251_0 conda-forge ```

CarlottaSartore commented 10 months ago

I saw that even forcing the version of urdf parser py does not change the outcome, see https://github.com/CarlottaSartore/ADAM/actions/runs/6783418213. And the version is equal if the package is downloaded with pip or conda.

CarlottaSartore commented 10 months ago

C.C. @traversaro @Nicogene

traversaro commented 10 months ago

urdf-parser-py from PyPI is not supported by the urdf-parser-py's mantainers and containing a really old and unsupported version (see https://github.com/ros/urdf_parser_py/issues/79#issuecomment-1626244210 and https://github.com/ami-iit/ADAM/issues/36). If you are already using conda, can you install urdf-parser-py from the urdfdom-py conda-forge package?

CarlottaSartore commented 10 months ago

In my computer I have installed urdf-parser-py from pip so maybe is the conda installation that creates issues. I am trying now to replicate a fresh installation as the one of the CI to check where is the issue

traversaro commented 10 months ago

This is an output of a CI (see https://github.com/CarlottaSartore/ADAM/actions/runs/6783258175),

Looking to the output here, the only error I see a lot of:

E   ModuleNotFoundError: No module named 'git'

I can't find the error that you mentioned in the original post.

CarlottaSartore commented 10 months ago

I am able to replicate the error, the difference as @traversaro said is in using urdf-parser-py from pip (no error) or urdfdom-py and the error appears: 

../../../miniforge3/envs/ADAM_env/lib/python3.10/site-packages/_pytest/runner.py:341: in from_call
    result: Optional[TResult] = func()
../../../miniforge3/envs/ADAM_env/lib/python3.10/site-packages/_pytest/runner.py:372: in <lambda>
    call = CallInfo.from_call(lambda: list(collector.collect()), "collect")
../../../miniforge3/envs/ADAM_env/lib/python3.10/site-packages/_pytest/python.py:531: in collect
    self._inject_setup_module_fixture()
../../../miniforge3/envs/ADAM_env/lib/python3.10/site-packages/_pytest/python.py:545: in _inject_setup_module_fixture
    self.obj, ("setUpModule", "setup_module")
../../../miniforge3/envs/ADAM_env/lib/python3.10/site-packages/_pytest/python.py:310: in obj
    self._obj = obj = self._getobj()
../../../miniforge3/envs/ADAM_env/lib/python3.10/site-packages/_pytest/python.py:528: in _getobj
    return self._importtestmodule()
../../../miniforge3/envs/ADAM_env/lib/python3.10/site-packages/_pytest/python.py:617: in _importtestmodule
    mod = import_path(self.path, mode=importmode, root=self.config.rootpath)
../../../miniforge3/envs/ADAM_env/lib/python3.10/site-packages/_pytest/pathlib.py:567: in import_path
    importlib.import_module(module_name)
../../../miniforge3/envs/ADAM_env/lib/python3.10/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:1050: in _gcd_import
    ???
<frozen importlib._bootstrap>:1027: in _find_and_load
    ???
<frozen importlib._bootstrap>:1006: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:688: in _load_unlocked
    ???
../../../miniforge3/envs/ADAM_env/lib/python3.10/site-packages/_pytest/assertion/rewrite.py:186: in exec_module
    exec(co, module.__dict__)
tests/parametric/test_CasADi_computations_parametric.py:58: in <module>
    comp = KinDynComputations(model_path, joints_name_list, root_link)
src/adam/casadi/computations.py:35: in __init__
    factory = URDFModelFactory(path=urdfstring, math=math)
src/adam/model/std_factories/std_model.py:24: in __init__
    self.urdf_desc = urdf_parser_py.urdf.URDF.from_xml_file(path)
../../../miniforge3/envs/ADAM_env/lib/python3.10/site-packages/urdf_parser_py/xml_reflection/core.py:617: in from_xml_file
    return cls.from_xml_string(xml_string)
../../../miniforge3/envs/ADAM_env/lib/python3.10/site-packages/urdf_parser_py/xml_reflection/core.py:610: in from_xml_string
    node = etree.fromstring(xml_string)
src/lxml/etree.pyx:3257: in lxml.etree.fromstring
    ???
src/lxml/parser.pxi:1911: in lxml.etree._parseMemoryDocument
    ???
E   ValueError: Unicode strings with encoding declaration are not supported. Please use bytes input or XML fragments without declaration.
CarlottaSartore commented 10 months ago

This is an output of a CI (see https://github.com/CarlottaSartore/ADAM/actions/runs/6783258175),

Looking to the output here, the only error I see a lot of:

E   ModuleNotFoundError: No module named 'git'

I can't find the error that you mentioned in the original post.

Sorry, wrong CI, I was talking about this https://github.com/CarlottaSartore/ADAM/actions/runs/6783316462/job/18437290808#step:7:964

traversaro commented 10 months ago

I was able to replicate the problem just with urdfdom-py:

mamba create -n urdfdom-py urdfdom-py
mamba activate urdfdom-py
wget https://raw.githubusercontent.com/icub-tech-iit/ergocub-gazebo-simulations/1179630a88541479df51ebb108a21865ea251302/models/stickBot/model.urdf
$CONDA_PREFIX/lib/urdfdom_py/display_urdf model.urdf

fails with:

Traceback (most recent call last):
  File "/home/traversaro/miniforge3/envs/urdfdom-py/lib/urdfdom_py/display_urdf", line 33, in <module>
    sys.exit(load_entry_point('urdfdom-py==1.2.1', 'console_scripts', 'display_urdf')())
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/traversaro/miniforge3/envs/urdfdom-py/lib/python3.12/site-packages/urdf_parser_py/display_urdf.py", line 15, in main
    robot = URDF.from_xml_string(args.file.read())
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/traversaro/miniforge3/envs/urdfdom-py/lib/python3.12/site-packages/urdf_parser_py/xml_reflection/core.py", line 610, in from_xml_string
    node = etree.fromstring(xml_string)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "src/lxml/etree.pyx", line 3257, in lxml.etree.fromstring
  File "src/lxml/parser.pxi", line 1911, in lxml.etree._parseMemoryDocument
ValueError: Unicode strings with encoding declaration are not supported. Please use bytes input or XML fragments without declaration.

mamba list:

(urdfdom-py) traversaro@IITICUBLAP257:~$ mamba list
# packages in environment at /home/traversaro/miniforge3/envs/urdfdom-py:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
bzip2                     1.0.8                hd590300_5    conda-forge
ca-certificates           2023.7.22            hbcca054_0    conda-forge
icu                       73.2                 h59595ed_0    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
libexpat                  2.5.0                hcb278e6_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.2.0               h807b86a_2    conda-forge
libgomp                   13.2.0               h807b86a_2    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libsqlite                 3.44.0               h2797004_0    conda-forge
libstdcxx-ng              13.2.0               h7e041cc_2    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libxml2                   2.11.5               h232c23b_1    conda-forge
libxslt                   1.1.37               h0054252_1    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
lxml                      4.9.3           py312he528aba_1    conda-forge
ncurses                   6.4                  h59595ed_2    conda-forge
openssl                   3.1.4                hd590300_0    conda-forge
pip                       23.3.1             pyhd8ed1ab_0    conda-forge
python                    3.12.0          hab00c5b_0_cpython    conda-forge
python_abi                3.12                    4_cp312    conda-forge
pyyaml                    6.0.1           py312h98912ed_1    conda-forge
readline                  8.2                  h8228510_1    conda-forge
setuptools                68.2.2             pyhd8ed1ab_0    conda-forge
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tzdata                    2023c                h71feb2d_0    conda-forge
urdfdom-py                1.2.1           py312h7900ff3_3    conda-forge
wheel                     0.41.3             pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
traversaro commented 10 months ago

I think it is a problem in urdf_parser_py and/or adam, but anyhow just removing encoding='UTF-8' I guess should be safe.

traversaro commented 10 months ago

I think it is a problem in urdf_parser_py and/or adam, but anyhow just removing encoding='UTF-8' I guess should be safe.

I opened the issue upstream in https://github.com/ros/urdf_parser_py/issues/82, while I guess to solve the issue in our models we can just get rid of encoding='UTF-8' from the top of our XML files, that anyhow I guess are just using ASCII characters so the encoding is not particularly useful.

CarlottaSartore commented 10 months ago

Yes I think also that removing https://github.com/icub-tech-iit/ergocub-gazebo-simulations/blob/1179630a88541479df51ebb108a21865ea251302/models/stickBot/model.urdf#L1 should be enough (also because generally in icub-models we do not have it), the only problem is that this entry is automatically generated when saving the urdf file e.g.
https://github.com/icub-tech-iit/ergocub-gazebo-simulations/blob/1179630a88541479df51ebb108a21865ea251302/scripts/modify_robot.py#L13 Am I right ? @Nicogene

traversaro commented 10 months ago

Argh, so this is a urdfpy/urchin (see https://github.com/fishbotics/urchin/blob/5a8068a9c6f4c0d43a57d6bdb4c9be52d9fd0549/urchin/urdf.py#L3714) + urdf_parser_py combined bug, great.

traversaro commented 10 months ago

Probably a quick fix on our side (i.e. ergocub-gazebo-simulations) is to re-parse the xml read from filename, and re-export removing the encoding, i.e. with tree.write(file_obj, pretty_print=True, xml_declaration=True) or tree.write(file_obj, pretty_print=True, xml_declaration=False)?

Nicogene commented 10 months ago

Yes I think also that removing

https://github.com/icub-tech-iit/ergocub-gazebo-simulations/blob/1179630a88541479df51ebb108a21865ea251302/models/stickBot/model.urdf#L1

should be enough (also because generally in icub-models we do not have it), the only problem is that this entry is automatically generated when saving the urdf file e.g.

https://github.com/icub-tech-iit/ergocub-gazebo-simulations/blob/1179630a88541479df51ebb108a21865ea251302/scripts/modify_robot.py#L13

Am I right ? @Nicogene

I have not memory of this, I know that the stickbot has been created by hand by @AlexAntn and @GrmanRodriguez, but I don't know modify_robot.py adds it the encoding on top

traversaro commented 10 months ago

I have not memory of this, I know that the stickbot has been created by hand by @AlexAntn and @GrmanRodriguez, but I don't know modify_robot.py adds it the encoding on top

No, the encoding is happening inside the urdfpy/urchin at the line https://github.com/fishbotics/urchin/blob/5a8068a9c6f4c0d43a57d6bdb4c9be52d9fd0549/urchin/urdf.py#L3714 . Another possible option is that adam removes the encoding line (or directly all the xml declaration line). That probably make also more sense as the bugged library (urdf_parser_py) is used on the adam side, so it make sense that the workaround is on that side.

CarlottaSartore commented 10 months ago

Done in https://github.com/CarlottaSartore/ADAM/commit/5bec8244823cbb87e864b2d5e5692b7227401d8e, now the CI passes.

What do we want to do with this issue then?

traversaro commented 10 months ago

What do we want to do with this issue then?

I think we can close it. An XML file that starts with <?xml version='1.0' encoding='UTF-8'?> is perfectly legal from the XML point of view, and urdf_parser_py should be able to handle that, and that is a bug that is tracked in https://github.com/ros/urdf_parser_py/issues/82 .

CarlottaSartore commented 10 months ago

Closing this issue then! Thanks everybody !